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R version 2.9.0 Under development (unstable) (2009-01-23 r47697)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ##--- S4 Methods (and Classes)
> options(useFancyQuotes=FALSE)
> library(methods)
> ##too fragile: showMethods(where = "package:methods")
>
> ##-- S4 classes with S3 slots [moved from ./reg-tests-1.R]
> setClass("test1", representation(date="POSIXct"))
[1] "test1"
> x <- new("test1", date=as.POSIXct("2003-10-09"))
> stopifnot(format(x @ date) == "2003-10-09")
> ## line 2 failed in 1.8.0 because of an extraneous space in "%in%"
>
> stopifnot(all.equal(3:3, 3.), all.equal(1., 1:1))
>
> ## trace (requiring methods):
> f <- function(x, y) { c(x,y)}
> xy <- 0
> trace(f, quote(x <- c(1, x)), exit = quote(xy <<- x), print = FALSE)
[1] "f"
> fxy <- f(2,3)
> stopifnot(identical(fxy, c(1,2,3)))
> stopifnot(identical(xy, c(1,2)))
> untrace(f)
>
> ## a generic and its methods
>
> setGeneric("f")
[1] "f"
> setMethod("f", c("character", "character"), function(x, y) paste(x,y))
[1] "f"
>
> ## trace the generic
> trace("f", quote(x <- c("A", x)), exit = quote(xy <<- c(x, "Z")), print = FALSE)
[1] "f"
>
> ## should work for any method
>
> stopifnot(identical(f(4,5), c("A",4,5)),
+ identical(xy, c("A", 4, "Z")))
>
> stopifnot(identical(f("B", "C"), paste(c("A","B"), "C")),
+ identical(xy, c("A", "B", "Z")))
>
> ## trace a method
> trace("f", sig = c("character", "character"), quote(x <- c(x, "D")),
+ exit = quote(xy <<- xyy <<- c(x, "W")), print = FALSE)
[1] "f"
>
> stopifnot(identical(f("B", "C"), paste(c("A","B","D"), "C")))
> stopifnot(identical(xyy, c("A", "B", "D", "W")))
> # got broken by Luke's lexical scoping fix:
> #stopifnot(identical(xy, xyy))
>
> ## but the default method is unchanged
> stopifnot(identical(f(4,5), c("A",4,5)),
+ identical(xy, c("A", 4, "Z")))
>
> removeGeneric("f")
[1] TRUE
> ## end of moved from trace.Rd
>
>
> ## print/show dispatch [moved from ./reg-tests-2.R ]
> ## The results have waffled back and forth.
> ## Currently (R 2.4.0) the intent is that automatic printing of S4
> ## objects should correspond to a call to show(), as per the green
> ## book, p. 332. Therefore, the show() method is called, once defined,
> ## for auto-printing foo, regardless of the S3 or S4 print() method.
> setClass("bar", representation(a="numeric"))
[1] "bar"
> foo <- new("bar", a=pi)
> foo
An object of class "bar"
Slot "a":
[1] 3.141593

> show(foo)
An object of class "bar"
Slot "a":
[1] 3.141593

> print(foo)
An object of class "bar"
Slot "a":
[1] 3.141593

>
> setMethod("show", "bar", function(object){cat("show method\n")})
[1] "show"
> show(foo)
show method
> foo
show method
> print(foo)
show method
> # suppressed because output depends on current choice of S4 type or
> # not. Can reinstate when S4 type is obligatory
> # print(foo, digits = 4)
>
> print.bar <- function(x, ...) cat("print method\n")
> foo
show method
> print(foo)
print method
> show(foo)
show method
>
> setMethod("print", "bar", function(x, ...){cat("S4 print method\n")})
Creating a new generic function for "print" in ".GlobalEnv"
[1] "print"
> foo
show method
> print(foo)
S4 print method
> show(foo)
show method
> ## calling print() with more than one argument suppresses the show()
> ## method, largely to prevent an infinite loop if there is in fact no
> ## show() method for this class. A better solution would be desirable.
> print(foo, digits = 4)
S4 print method
>
> setClassUnion("integer or NULL", members = c("integer","NULL"))
[1] "integer or NULL"
> setClass("c1", representation(x = "integer", code = "integer or NULL"))
[1] "c1"
> nc <- new("c1", x = 1:2)
> str(nc)# gave ^ANULL^A in 2.0.0
Formal class 'c1' [package ".GlobalEnv"] with 2 slots
  ..@ x : int [1:2] 1 2
  ..@ code: NULL
> ##
>
>
> library(stats4)
> showMethods("coerce", classes=c("matrix", "numeric"))
Function: coerce (package methods)
from="ANY", to="matrix"
from="ANY", to="numeric"

> ## {gave wrong result for a while in R 2.4.0}
>
> ## the following showMethods() output tends to generate errors in the tests
> ## whenever the contents of the packages change. Searching in the
> ## diff's can easily mask real problems. If there is a point
> ## to the printout, e.g., to verify that certain methods exist,
> ## hasMethod() would be a useful replacement
>
> ## showMethods(where = "package:stats4")
> ## showMethods("show")
> ## showMethods("show")
> ## showMethods("plot") # (ANY,ANY) and (profile.mle, missing)
> ## showMethods(classes="mle")
> ## showMethods(classes="matrix")
>
>
> ##--- "[" fiasco before R 2.2.0 :
> d2 <- data.frame(b= I(matrix(1:6,3,2)))
> ## all is well:
> d2[2,]
     [,1] [,2]
[1,] 2 5
> stopifnot(identical(d2[-1,], d2[2:3,]))
> ## Now make "[" into S4 generic by defining a trivial method
> setClass("Mat", representation(Dim = "integer", "VIRTUAL"))
[1] "Mat"
> setMethod("[", signature(x = "Mat",
+ i = "missing", j = "missing", drop = "ANY"),
+ function (x, i, j, drop) x)
[1] "["
> ## Can even remove the method: it doesn't help
> removeMethod("[", signature(x = "Mat",
+ i = "missing", j = "missing", drop = "ANY"))
[1] TRUE
> d2[1:2,] ## used to fail badly; now okay
     [,1] [,2]
[1,] 1 4
[2,] 2 5
> stopifnot(identical(d2[-1,], d2[2:3,]))
> ## failed in R <= 2.1.x
>
>
> ## Fritz' S4 "odditiy"
> setClass("X", representation(bar="numeric"))
[1] "X"
> setClass("Y", contains="X")
[1] "Y"
> ## Now we define a generic foo() and two different methods for "X" and
> ## "Y" objects for arg missing:
> setGeneric("foo", function(object, arg) standardGeneric("foo"))
[1] "foo"
> setMethod("foo", signature(object= "X", arg="missing"),
+ function(object, arg) cat("an X object with bar =", object@bar, "\n"))
[1] "foo"
> setMethod("foo", signature(object= "Y", arg="missing"),
+ function(object, arg) cat("a Y object with bar =", object@bar, "\n"))
[1] "foo"
> ## Finally we create a method where arg is "logical" only for class
> ## "X", hence class "Y" should inherit that:
> setMethod("foo", signature(object= "X", arg= "logical"),
+ function(object, arg) cat("Hello World!\n") )
[1] "foo"
> ## now create objects and call methods:
> y <- new("Y", bar=2)
> ## showMethods("foo")
> foo(y)
a Y object with bar = 2
> foo(y, arg=TRUE)## Hello World!
Hello World!
> ## OK, inheritance worked, and we have
> ## showMethods("foo")
> foo(y)
a Y object with bar = 2
> ## still 'Y' -- was 'X object' in R < 2.3
>
>
> ## Multiple inheritance
> setClass("A", representation(x = "numeric"))
[1] "A"
> setClass("B", representation(y = "character"))
[1] "B"
> setClass("C", contains = c("A", "B"), representation(z = "logical"))
[1] "C"
> new("C")
An object of class "C"
Slot "z":
logical(0)

Slot "x":
numeric(0)

Slot "y":
character(0)

> setClass("C", contains = c("A", "B"), representation(z = "logical"),
+ prototype = prototype(x = 1.5, y = "test", z = TRUE))
[1] "C"
> (cc <- new("C"))
An object of class "C"
Slot "z":
[1] TRUE

Slot "x":
[1] 1.5

Slot "y":
[1] "test"

> ## failed reconcilePropertiesAndPrototype(..) after svn r37018
>
>
> ## "Logic" group -- was missing in R <= 2.4.0
> stopifnot(all(getGroupMembers("Logic") %in% c("&", "|")),
+ any(getGroupMembers("Ops") == "Logic"))
> setClass("brob", contains="numeric")
[1] "brob"
> b <- new("brob", 3.14)
> logic.brob.error <- function(nm)
+ stop("logic operator '", nm, "' not applicable to brobs")
> logic2 <- function(e1,e2) logic.brob.error(.Generic)
> setMethod("Logic", signature("brob", "ANY"), logic2)
[1] "Logic"
> setMethod("Logic", signature("ANY", "brob"), logic2)
[1] "Logic"
> ## Now ensure that using group members gives error:
> assertError <- function(expr)
+ stopifnot(inherits(try(expr, silent = TRUE), "try-error"))
> assertWarning <- function(expr)
+ stopifnot(inherits(tryCatch(expr, warning = function(w)w), "warning"))
> assertWarning_atleast <- function(expr) {
+ r <- tryCatch(expr, warning = function(w)w, error = function(e)e)
+ stopifnot(inherits(r, "warning") || inherits(r, "error"))
+ }
>
> assertError(b & b)
Note: Method with signature "brob#ANY" chosen for function "&", target signature "brob#brob". "ANY#brob" would also be valid
> assertError(b | 1)
> assertError(TRUE & b)
>
>
> ## methods' hidden cbind() / rbind:
> cBind <- methods:::cbind
> setClass("myMat", representation(x = "numeric"))
[1] "myMat"
> setMethod("cbind2", signature(x = "myMat", y = "missing"), function(x,y) x)
[1] "cbind2"
> m <- new("myMat", x = c(1, pi))
> stopifnot(identical(m, cBind(m)))
>
>
> ## explicit print or show on a basic class with an S4 bit
> ## caused infinite recursion
> setClass("Foo", representation(name="character"), contains="matrix")
[1] "Foo"
> (f <- new("Foo", name="Sam", matrix()))
An object of class "Foo"
     [,1]
[1,] NA
Slot "name":
[1] "Sam"

> f2 <- new("Foo", .Data = diag(2), name="Diag")# explicit .Data
> (m <- as(f, "matrix"))
     [,1]
[1,] NA
> ## this has no longer (2.7.0) an S4 bit: set it explicitly just for testing:
> stopifnot(isS4(m. <- asS4(m)),
+ identical(m, f@.Data))
> show(m.)
     [,1]
[1,] NA
> print(m.)
     [,1]
[1,] NA
> ## fixed in 2.5.0 patched
>
> ## callGeneric inside a method with new arguments {hence using .local()}:
> setGeneric("Gfun", function(x, ...) standardGeneric("Gfun"),
+ useAsDefault = function(x, ...) sum(x, ...))
[1] "Gfun"
> setClass("myMat", contains="matrix")
[1] "myMat"
> setClass("mmat2", contains="matrix")
[1] "mmat2"
> setClass("mmat3", contains="mmat2")
[1] "mmat3"
> setMethod(Gfun, signature(x = "myMat"),
+ function(x, extrarg = TRUE) {
+ cat("in 'myMat' method for 'Gfun() : extrarg=", extrarg, "\n")
+ Gfun(unclass(x))
+ })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gfun, signature(x = "mmat2"),
+ function(x, extrarg = TRUE) {
+ cat("in 'mmat2' method for 'Gfun() : extrarg=", extrarg, "\n")
+ x <- unclass(x)
+ callGeneric()
+ })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gfun, signature(x = "mmat3"),
+ function(x, extrarg = TRUE) {
+ cat("in 'mmat3' method for 'Gfun() : extrarg=", extrarg, "\n")
+ x <- as(x, "mmat2")
+ callGeneric()
+ })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> wrapG <- function(x, a1, a2) {
+ myextra <- missing(a1) && missing(a2)
+ Gfun(x, extrarg = myextra)
+ }
>
> (mm <- new("myMat", diag(3)))
An object of class "myMat"
     [,1] [,2] [,3]
[1,] 1 0 0
[2,] 0 1 0
[3,] 0 0 1
> Gfun(mm)
in 'myMat' method for 'Gfun() : extrarg= TRUE
[1] 3
> stopifnot(identical(wrapG(mm), Gfun(mm, TRUE)),
+ identical(wrapG(mm,,2), Gfun(mm, FALSE)))
in 'myMat' method for 'Gfun() : extrarg= TRUE
in 'myMat' method for 'Gfun() : extrarg= TRUE
in 'myMat' method for 'Gfun() : extrarg= FALSE
in 'myMat' method for 'Gfun() : extrarg= FALSE
>
> Gfun(mm, extrarg = FALSE)
in 'myMat' method for 'Gfun() : extrarg= FALSE
[1] 3
> m2 <- new("mmat2", diag(3))
> Gfun(m2)
in 'mmat2' method for 'Gfun() : extrarg= TRUE
[1] 3
> Gfun(m2, extrarg = FALSE)
in 'mmat2' method for 'Gfun() : extrarg= FALSE
[1] 3
> ## The last two gave Error ...... variable ".local" was not found
> (m3 <- new("mmat3", diag(3)))
An object of class "mmat3"
     [,1] [,2] [,3]
[1,] 1 0 0
[2,] 0 1 0
[3,] 0 0 1
> Gfun(m3)
in 'mmat3' method for 'Gfun() : extrarg= TRUE
in 'mmat2' method for 'Gfun() : extrarg= TRUE
[1] 3
> Gfun(m3, extrarg = FALSE) # used to not pass 'extrarg'
in 'mmat3' method for 'Gfun() : extrarg= FALSE
in 'mmat2' method for 'Gfun() : extrarg= FALSE
[1] 3
>
> ## -- a variant of the above which failed in version <= 2.5.1 :
> setGeneric("Gf", function(x, ...) standardGeneric("Gf"))
[1] "Gf"
> setMethod(Gf, signature(x = "mmat2"),
+ function(x, ...) {
+ cat("in 'mmat2' method for 'Gf()\n")
+ x <- unclass(x)
+ callGeneric()
+ })
[1] "Gf"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gf, signature(x = "mmat3"),
+ function(x, ...) {
+ cat("in 'mmat3' method for 'Gf()\n")
+ x <- as(x, "mmat2")
+ callGeneric()
+ })
[1] "Gf"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gf, signature(x = "matrix"),
+ function(x, a1, ...) {
+ cat(sprintf("matrix %d x %d ...\n", nrow(x), ncol(x)))
+ list(x=x, a1=a1, ...)
+ })
[1] "Gf"
attr(,"package")
[1] ".GlobalEnv"
>
> wrap2 <- function(x, a1, ...) {
+ A1 <- if(missing(a1)) "A1" else as.character(a1)
+ Gf(x, ..., a1 = A1)
+ }
> ## Gave errors in R 2.5.1 :
> wrap2(m2, foo = 3.14)
in 'mmat2' method for 'Gf()
matrix 3 x 3 ...
$x
     [,1] [,2] [,3]
[1,] 1 0 0
[2,] 0 1 0
[3,] 0 0 1

$a1
[1] "A1"

$foo
[1] 3.14

> wrap2(m2, 10, answer.all = 42)
in 'mmat2' method for 'Gf()
matrix 3 x 3 ...
$x
     [,1] [,2] [,3]
[1,] 1 0 0
[2,] 0 1 0
[3,] 0 0 1

$a1
[1] "10"

$answer.all
[1] 42

>
>
> ## regression tests of dispatch: most of these became primitive in 2.6.0
> setClass("c1", "numeric")
[1] "c1"
> setClass("c2", "numeric")
[1] "c2"
> x_c1 <- new("c1")
> # the next failed < 2.5.0 as the signature in .BasicFunsList was wrong
> setMethod("as.character", "c1", function(x, ...) "fn test")
[1] "as.character"
> as.character(x_c1)
[1] "fn test"
>
> setMethod("as.integer", "c1", function(x, ...) 42)
[1] "as.integer"
> as.integer(x_c1)
[1] 42
>
> setMethod("as.logical", "c1", function(x, ...) NA)
[1] "as.logical"
> as.logical(x_c1)
[1] NA
>
> setMethod("as.complex", "c1", function(x, ...) pi+0i)
[1] "as.complex"
> as.complex(x_c1)
[1] 3.141593+0i
>
> setMethod("as.raw", "c1", function(x) as.raw(10))
[1] "as.raw"
> as.raw(x_c1)
[1] 0a
>
> # as.double, as.real use as.numeric for their methods to maintain equivalence
> setMethod("as.numeric", "c1", function(x, ...) 42+pi)
[1] "as.numeric"
> identical(as.numeric(x_c1),as.double(x_c1))
[1] TRUE
> identical(as.numeric(x_c1),as.real(x_c1))
[1] TRUE
>
>
> setMethod(as.double, "c2", function(x, ...) x@.Data+pi)
[1] "as.numeric"
> x_c2 <- new("c2", pi)
> identical(as.numeric(x_c2),as.double(x_c2))
[1] TRUE
> identical(as.numeric(x_c2),as.real(x_c2))
[1] TRUE
>
> ## '!' changed signature from 'e1' to 'x' in 2.6.0
> setClass("foo", "logical")
[1] "foo"
> setMethod("!", "foo", function(e1) e1+NA)
[1] "!"
Warning message:
For function "!", signature "foo": argument in method definition changed from (e1) to (x)
> selectMethod("!", "foo")
Method Definition:

function (x)
x + NA

Signatures:
        x
target "foo"
defined "foo"
> xx <- new("foo", FALSE)
> !xx
An object of class "foo"
[1] NA
>
> ## This failed for about one day -- as.vector(x, mode) :
> setMethod("as.vector", signature(x = "foo", mode = "missing"),
+ function(x) unclass(x))
Creating a new generic function for "as.vector" in ".GlobalEnv"
[1] "as.vector"
> ## whereas this fails in R versions earlier than 2.6.0:
> setMethod("as.vector", "foo", function(x) unclass(x))# gives message
In method for function "as.vector": expanding the signature to
include omitted arguments in definition: mode = "missing"
[1] "as.vector"
>
> ## stats4::AIC in R < 2.7.0 used to clobber stats::AIC
> pfit <- function(data) {
+ m <- mean(data)
+ loglik <- sum(dpois(data, m))
+ ans <- list(par = m, loglik = loglik)
+ class(ans) <- "pfit"
+ ans
+ }
> AIC.pfit <- function(object, ..., k = 2) -2*object$loglik + k
> AIC(pfit(1:10))
[1] 0.05867604
> library(stats4) # and keep on search() for tests below
> AIC(pfit(1:10)) # failed in R < 2.7.0
[1] 0.05867604
>
> ## For a few days (~ 2008-01-30), this failed to work without any notice:
> setClass("Mat", representation(Dim = "integer","VIRTUAL"))
[1] "Mat"
> setClass("dMat", representation(x = "numeric", "VIRTUAL"), contains = "Mat")
[1] "dMat"
> setClass("CMat", representation(dnames = "list","VIRTUAL"), contains = "Mat")
[1] "CMat"
> setClass("dCMat", contains = c("dMat", "CMat"))
[1] "dCMat"
> stopifnot(!isVirtualClass("dCMat"),
+ length(slotNames(new("dCMat"))) == 3)
>
>
> ## Passing "..." arguments in nested callGeneric()s
> setClass("m1", contains="matrix")
[1] "m1"
> setClass("m2", contains="m1")
[1] "m2"
> setClass("m3", contains="m2")
[1] "m3"
> ##
> setGeneric("foo", function(x, ...) standardGeneric("foo"))
[1] "foo"
> setMethod("foo", signature(x = "m1"),
+ function(x, ...) cat(" <m1> ", format(match.call()),"\n"))
[1] "foo"
> setMethod("foo", signature(x = "m2"),
+ function(x, ...) {
+ cat(" <m2> ", format(match.call()),"\n")
+ x <- as(x, "m1"); callGeneric()
+ })
[1] "foo"
> setMethod("foo", signature(x = "m3"),
+ function(x, ...) {
+ cat(" <m3> ", format(match.call()),"\n")
+ x <- as(x, "m2"); callGeneric()
+ })
[1] "foo"
> foo(new("m1"), bla = TRUE)
 <m1> foo(x = new("m1"), bla = TRUE)
> foo(new("m2"), bla = TRUE)
 <m2> foo(x = new("m2"), bla = TRUE)
 <m1> foo(x = x, bla = TRUE)
> foo(new("m3"), bla = TRUE)
 <m3> foo(x = new("m3"), bla = TRUE)
 <m2> foo(x = x, bla = TRUE)
 <m1> foo(x = x, bla = TRUE)
> ## The last one used to loose 'bla = TRUE' {the "..."} when it got to m1
>
> ## is() for S3 objects with multiple class strings
> setClassUnion("OptionalPOSIXct", c("POSIXct", "NULL"))
[1] "OptionalPOSIXct"
> stopifnot(is(Sys.time(), "OptionalPOSIXct"))
> ## failed in R 2.7.0
>
> ## getGeneric() / getGenerics() "problems" related to 'tools' usage:
> e4 <- as.environment("package:stats4")
> gg4 <- getGenerics(e4)
> stopifnot(c("BIC", "coef", "confint", "logLik", "plot", "profile",
+ "show", "summary", "update", "vcov") %in% gg4, # %in% : "future proof"
+ unlist(lapply(gg4, function(g) !is.null(getGeneric(g, where = e4)))),
+ unlist(lapply(gg4, function(g) !is.null(getGeneric(g)))))
> em <- as.environment("package:methods")
> ggm <- getGenerics(em)
> gms <- c("addNextMethod", "body<-", "cbind2", "initialize",
+ "loadMethod", "Math", "Ops", "rbind2", "show")
> stopifnot(unlist(lapply(ggm, function(g) !is.null(getGeneric(g, where = em)))),
+ unlist(lapply(ggm, function(g) !is.null(getGeneric(g)))),
+ gms %in% ggm,
+ gms %in% tools:::get_S4_generics_with_methods(em), # with "message"
+ ## all above worked in 2.7.0, however:
+ isGeneric("show", where=e4),
+ hasMethods("show", where=e4), hasMethods("show", where=em),
+ ## isGeneric("dim", where=as.environment("package:Matrix"))
+ identical(as.character(gg4), #gg4 has packages attr.; tools::: doesn't
+ tools:::get_S4_generics_with_methods(e4))
+ )
> ## the last failed in R 2.7.0 : was not showing "show"
> ## TODO: use "Matrix" checks once that is >= 1.0
>
> ## containing "array" ("matrix", "ts", ..)
> t. <- ts(1:10, frequency = 4, start = c(1959, 2))
> setClass("Arr", contains= "array"); x <- new("Arr", cbind(17))
[1] "Arr"
> setClass("Ts", contains= "ts"); tt <- new("Ts", t.); t2 <- as(t., "Ts")
[1] "Ts"
> setClass("ts2", representation(x = "Ts", y = "ts"))
[1] "ts2"
> tt2 <- new("ts2", x=t2, y=t.)
> stopifnot(dim(x) == c(1,1), is(tt, "ts"), is(t2, "ts"),
+ ## FIXME: identical(tt, t2)
+ length(tt) == length(t.),
+ identical(tt2@x, t2), identical(tt2@y, t.))
> ## new(..) failed in R 2.7.0
>
> ## Method with wrong argument order :
> setGeneric("test1", function(x, printit = TRUE, name = "tmp")
+ standardGeneric("test1"))
[1] "test1"
> assertWarning_atleast(
+ setMethod("test1", "numeric", function(x, name, printit) match.call())
+ )## did not warn or error in R 2.7.0 and earlier
>
> library(stats4)
> c1 <- getClass("mle", where = "stats4")
> c2 <- getClass("mle", where = "package:stats4")
> s1 <- getMethod("summary", "mle", where = "stats4")
> s2 <- getMethod("summary", "mle", where = "package:stats4")
> stopifnot(is(c1, "classRepresentation"),
+ is(s1, "MethodDefinition"),
+ identical(c1,c2), identical(s1,s2))
> ## failed at times in the past
>
> ## Extending "matrix", the .Data slot etc:
> setClass("moo", representation("matrix"))
[1] "moo"
> m <- matrix(1:4, 2, dimnames= list(NULL, c("A","B")))
> nf <- new("moo", .Data = m)
> n2 <- new("moo", 3:1, 3,2)
> n3 <- new("moo", 1:6, ncol=2)
> stopifnot(identical(m, as(nf, "matrix")),
+ identical(matrix(3:1,3,2), as(n2, "matrix")),
+ identical(matrix(1:6,ncol=2), as(n3, "matrix")))
> ## partly failed at times in pre-2.8.0
>
> ## "[" subsetting of "simple S4" classes:
> for(bcl in c("list","integer","numeric")) {
+ setClass("C", contains= bcl)
+ x <- new("C", 1:3); x <- x[2:3]
+ stopifnot(is(x, "C"), is(rep(x, 3), "C"), is(rep.int(x, 2), "C"))
+ }
> ## used to drop the class in 2.8.0 and earlier
>
> ##From "Michael Lawrence" <....@fhcrc.org> To r-devel@r-project, 25 Nov 2008:
> setGeneric("order", signature="...",
+ function (..., na.last=TRUE, decreasing=FALSE)
+ standardGeneric("order"))
Creating a generic for "order" in package ".GlobalEnv"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (na.last, decreasing))
[1] "order"
> stopifnot(identical(rbind(1), matrix(1,1,1)))
> setGeneric("rbind", function(..., deparse.level=1)
+ standardGeneric("rbind"), signature = "...")
Creating a generic for "rbind" in package ".GlobalEnv"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (deparse.level))
[1] "rbind"
> stopifnot(identical(rbind(1), matrix(1,1,1)))
> ## gave Error in .Method( .... in R 2.8.0
>
> ## median.default( <simple S4> )
> ## FIXME: if we use "C" instead of "L", this fails because of caching
> setClass("L", contains = "list")
[1] "L"
> ## {simplistic, just for the sake of testing here} :
> setMethod("Compare", signature(e1="L", e2="ANY"),
+ function(e1,e2) sapply(e1, .Generic, e2=e2))
[1] "Compare"
> setMethod("Summary", "L",
+ function(x, ..., na.rm=FALSE) {x <- unlist(x); callNextMethod()})
[1] "Summary"
> setMethod("[", signature(x="L", i="ANY", j="missing",drop="missing"),
+ function(x,i,j,drop) new("L", x@.Data[i]))
[1] "["
> x <- new("L", 1:3); x2 <- x[-2]
> stopifnot(unlist(x2) == (1:3)[-2],
+ is(mx <- median(x), "L"), mx == 2,
+ identical(mx, quantile(x, 0.5, names=FALSE)),
+ ## median of two -> sum()
+ median(x2) == 2)
> ## median.default(x) was too stringent on x
>
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